Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri; Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri.
Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, Missouri; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri.
Biophys J. 2020 Jul 21;119(2):402-418. doi: 10.1016/j.bpj.2020.06.014. Epub 2020 Jun 23.
Phase separation is thought to underlie spatial and temporal organization that is required for controlling biochemical reactions in cells. Multivalence of interaction motifs, also known as stickers, is a defining feature of proteins that drive phase separation. Intrinsically disordered proteins with stickers uniformly distributed along the linear sequence can serve as scaffold molecules that drive phase separation. The sequence-intrinsic contributions of disordered proteins to phase separation can be discerned by computing or measuring sequence-specific phase diagrams. These help to delineate the combinations of protein concentration and a suitable control parameter, such as temperature, that support phase separation. Here, we present an approach that combines detailed simulations with a numerical adaptation of an analytical Gaussian cluster theory to enable the calculation of sequence-specific phase diagrams. Our approach leverages the known equivalence between the driving forces for single-chain collapse in dilute solutions and the driving forces for phase separation in concentrated solutions. We demonstrate the application of the theory-aided computations through calculation of phase diagrams for a set of archetypal intrinsically disordered low-complexity domains. We also leverage theories to compute sequence-specific percolation lines and thereby provide a thermodynamic framework for hardening transitions that have been observed for many biomolecular condensates.
相分离被认为是控制细胞内生化反应所需的空间和时间组织的基础。相互作用基序的多价性，也称为贴纸，是驱动相分离的蛋白质的一个定义特征。具有贴纸的均匀分布在线性序列上的无规卷曲蛋白质可以作为支架分子来驱动相分离。通过计算或测量序列特异性相图，可以辨别无规卷曲蛋白质对相分离的序列固有贡献。这些相图有助于描绘支持相分离的蛋白质浓度和合适控制参数（如温度）的组合。在这里，我们提出了一种结合详细模拟和分析高斯团理论的数值适配的方法，以实现序列特异性相图的计算。我们的方法利用了在稀溶液中单链塌陷的驱动力与浓溶液中相分离的驱动力之间的已知等价性。我们通过计算一组典型的固有无序低复杂度结构域的相图来展示理论辅助计算的应用。我们还利用理论计算序列特异性渗透线，从而为许多生物分子凝聚物观察到的硬化转变提供热力学框架。
